Convert giotto Object to GiottoDB — as

A convenience function that coerces a giotto object to a GiottoDB object with a database backend. Expression matrices are converted to dbMatrix objects and spatial data are converted to dbSpatial objects.

Usage

as_giottodb(
  x,
  con = NULL,
  db_path = NULL,
  prefix = "gdb_",
  overwrite = FALSE,
  verbose = TRUE,
  temporary = TRUE
)

Arguments

x: A giotto object
con: A DBIConnection object from a duckdb::duckdb connection object
db_path: Path to the database file if creating a new persistent connection
prefix: A string prefix to add to database table names
overwrite: Whether to overwrite existing tables
verbose: Whether to print progress messages
temporary: if TRUE (default), will create a temporary table that is local to this connection and will be automatically deleted when con expires

Value

A GiottoDB object

Examples

if (FALSE) { # \dontrun{
library(GiottoDB)
library(dbSpatial)

# Create connection
con <- dbConnect(duckdb(), dbdir = ":memory:")
loadSpatial(con)

# Convert Giotto object
my_giotto_db <- as_giottodb(my_giotto, con = con)

# Don't forget to close the connection when done
dbDisconnect(con, shutdown = TRUE)
} # }